<<<<< Input Tree (Top_node = 29) >>>>>

( seq0020{28}:0.1529, ( seq0018{26}:0.1741, ( ( seq0015{23}:0.1492, ( seq0013{20}:0.1827, seq0014{21}:0.1659 ){22}:0.0049 ){24}:0.0297, ( ( seq0008{16}:0.0865, seq0009{17}:0.1286 ){18}:0.0335, ( ( seq0005{10}:0.0368, ( seq0006{11}:0.0286, seq0007{12}:0.0362 ){13}:0.0065 ){14}:0.0368, ( ( seq0000{1}:0.0054, seq0001{2}:0.0081 ){3}:0.0232, ( seq0002{4}:0.0189, ( seq0003{5}:0.0124, seq0004{6}:0.0108 ){7}:0.0070 ){8}:0.0270 ){9}:0.0205 ){15}:0.0703 ){19}:0.0383 ){25}:0.0314 ){27}:0.0130 ){29};


<<<<< Input MSA >>>>>

#{Sequences} = 15 .
#{Sites in the segment}_ref = 250 ,
#{Sites in the segment}_rec = 203 .


<< Correspondence between sequence IDs and sequence indices >>

Indx:	Seq_ID

0:	seq0000
1:	seq0001
2:	seq0002
3:	seq0003
4:	seq0004
5:	seq0005
6:	seq0006
7:	seq0007
8:	seq0008
9:	seq0009
10:	seq0013
11:	seq0014
12:	seq0015
13:	seq0018
14:	seq0020


<< Original Segment of the Reference Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        -AAAG------------------------------GATG-T-------------------
seq0001        -AAAG------------------------------GATG-T-------------------
seq0002        -AAAG------------------------------GATG-T-------------------
seq0003        -AAAG------------------------------GATG-T-------------------
seq0004        -AAAG------------------------------GATG-T-------------------
seq0005        -AAAG------------------------------GATGCT-------------------
seq0006        -AAAG------------------------------GATGCT-------------------
seq0007        -AAAG------------------------------GATGCT-------------------
seq0008        -AAAG------------------------------GACG-C-------------------
seq0009        -AAAG------------------------------GACG-C-------------------
seq0013        -CTCG------------------------------GACG-C-------------------
seq0014        -AAATGTGCTCACATGACCAAGCAGACATTTGATGGACG-T-------------------
seq0015        -CAAG------------------------------GACG-TGCACTGAACTGCTAGGAAT
seq0018        CAAAG------------------------------GTCG-T-------------------
seq0020        CAAAG------------------------------GAGG-T-------------------

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ---CGTGGCATTGT--TTTCCAAAGTCATTA-CATCTTAGAAGGTTCGTCCTGTCAGTTA
seq0001        ---CGTGGCATTGT--TTTCCAAAGTCATTA-CATCTTAGAAGGTTCGTCCTGTCAGTTA
seq0002        ---CGTGGCATTGT--TTTCCAAAGTCGTTA-CATCTTAGAAGGTGCGTCCTGTCAGTTA
seq0003        ---CGTGGCATTGT--TTTCCATAGTCGTTA-CATCTTA-AAGGTTCGTCCTGTCAGTTA
seq0004        ---CGTGGCATTGT--TTTCCATAGTCGTTA-CATCTTAGAAGGTTCGTCCTGTCAGTTA
seq0005        ---CGTGGCATTTT--ATTCCAAAGTCATTA-CAGCTTAGAAGGTATGTCCTGTCAGTTA
seq0006        ---CGTGGCATTTT--ATTCCAAGGTCATTT-CATCTTATAAGGTTCGTCCTGTCAGTTA
seq0007        ---CGTGGCATTTT--ATTCCAAGGTCAGTA-CATCTTATAAGGTTCATCCTGTCAGTTA
seq0008        ---CGTGGCATTAT--ATTCCAAAGTCATAA-CATCTTAATAAGTTCGTTC---------
seq0009        ---CGTGGCATTGT--ATCCCAAAGTCATTA-CATCTTATAATGCTCGCCCTGTCAGTTA
seq0013        ---CGAAACATTGTCGATTCCAAAATCATTA-TATCTGC--TTGTTGCTCCGGTCGG---
seq0014        ---CGTACCATT----CTGCTAATGCCAATA-AATCATCATTTTGTCGTACTGTCATTTA
seq0015        TCACGTAACATTGT--ATTCTAAGGTCAT-A-C------------------------TTA
seq0018        ---CGTAACATTGG--GTTGAAATGCCATTG-TGTCCTCACATGTTCGTTCTGTCGTTTA
seq0020        ---CGTAACGTTGT--ACTCAAATGTCATTCACCTCTTCAAATGTTGGTCGTGGCAGTTT

(position)     111111111111111111111111111111111111111111111111111111111111
               222222222233333333334444444444555555555566666666667777777777
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GCATCCATG-------------------------CCCTATGACCTGCATTAGAATCCAGA
seq0001        GCATCCATG-------------------------CCCTATGACATGCATTAGAATCCAGA
seq0002        GCATCCGTG-------------------------CCCTAGGACCTGCATTAGAATCCAGA
seq0003        GCATCCGTG-------------------------CCCTATGACCTGCATTAGAATGCCGA
seq0004        GCATCCGTG-------------------------CCCTATGACCTGCATTAGAATCCAGA
seq0005        GCATCCATG-------------------------CCGTATGACCTGCATTAGAATCCAGA
seq0006        GAATCCATG-------------------------CCGTATGACATGCAGTAGAATCCAGA
seq0007        GCTTCCATG-------------------------CCGTATGACCTGCATTAGAATCCAGA
seq0008        ------------------------------------CTATGACCTCCATTAGTA-CCAGA
seq0009        ACTTACCTG--------------------------ACT-GGACCTCCATTAGAG-CCAGA
seq0013        A-TGCCATGAATCCCCACACCTACTTAAACTGGC-ACAACGTCTTCCAGTAGGA-GCAGA
seq0014        GGTTCCAAG--------------------------ACTATGCCCTCCATTCGTA-GC-GA
seq0015        GCTTCCATG--------------------------ACTATGACCTCCATTAGAA-GCAGA
seq0018        GCTTCCATG--------------------------ACGAGAACCTTGATTCGCA--CAGA
seq0020        GCTTGAATG--------------------------ACTAAGGCGTCT-TTTGAA-GCAGA

(position)     111111111111111111112222222222222222222222222222222222222222
               888888888899999999990000000000111111111122222222223333333333
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ATGGCGAACCTCGACATTCCAGAG--GTTC------TCGTTTGACGGCCACTGCC---AT
seq0001        ATGGCGAACCTCGACATTCGAGAG--TTTC------TCGTTTGACGGCCACTGAC---AT
seq0002        ATGGCGATCCTCGATATTCGAGAG--GTTC------TCGTTTTACGGCCACTGAC---AT
seq0003        ATGGCGATCCTCGATATTCGAGAG--GTTC------TCGTTTGACGGCCACTGAC---AT
seq0004        ATGGCGATCCTCGATATTCGAGAG--GTTC------TCGTTTGACGGCCTCTGAC---AT
seq0005        ATGGCGGGCATCCATATACGAGAG--TTTC------TCGTTCGACGTCCACTGAC---AT
seq0006        ATGGCGGGCCTCCATATTCGGGAG--TTTC------TCGTTTGACGCCCACTGACGTCAT
seq0007        ATGGCGGGTCTCCATATTCGGGAG--TTTC------TCGTTTGACGTCCACTGACGTCAT
seq0008        ACGGCGACAGTCCACATTGGAGAG--CATC-----CTTGTTTGACGGCCACGG-------
seq0009        ATGGCGACAC-CCATAGTGGGCAG--CTTC-----CTTGATTGACTGCCCCGG-------
seq0013        CGCGCAAGGGCCCATATTACCGTGTCATTCCGCCA-TTGTTTGACGGCCACTG-------
seq0014        CTTGCGAGACTCCATATTTC----------------------------------------
seq0015        CTGGCGAGACTCCATATTTCAGAGGATTCC------TTGTATCACGGCCACTG-------
seq0018        CTGTCTACACTCCATATT-CAGAGTCTTTC------GTGCTTGACTGCCAATG-------
seq0020        CTGGCAATACTCCTTATT-GAGAGTCGCTC------TTGCCAGTCGGA-ACTG-------

(position)     2222222222
               4444444444
               0123456789
                         
seq0000        GTGCACAGAG
seq0001        GTGCACAGAG
seq0002        GTGCACAGAG
seq0003        GTGCACAGAG
seq0004        GTGCACAGAG
seq0005        GTGCCCAGAG
seq0006        GTGCCCAGAG
seq0007        GTGCCCAGAG
seq0008        CTGCACAGAG
seq0009        CTGCACAGAG
seq0013        CTCCACCGAG
seq0014        ----------
seq0015        CT--AAAGAG
seq0018        CTGCACAAAA
seq0020        CTGCACAGAG


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ------------AAAGGATG-TCGTGGCATTGTTTTCCAAAGTCATT-ACATCT--TAGA
seq0001        ------------AAAGGATG-TCGTGGCATTGTTTTCCAAAGTCATT-ACATCT--TAGA
seq0002        ------------AAAGGATG-TCGTGGCATTGTTTTCCAAAGTCGTT-ACATCT--TAGA
seq0003        ------------AAAGGATG-TCGTGGCATTGTTTTCCATAGTCGTT-ACATCT--TA-A
seq0004        ------------AAAGGATG-TCGTGGCATTGTTTTCCATAGTCGTT-ACATCT--TAGA
seq0005        ------------AAAGGATGCTCGTGGCATTTTATTCCAAAGTCATT-ACAGCT--TAGA
seq0006        ------------AAAGGATGCTCGTGGCATTTTATTCCAAGGTCATT-TCATCT--TATA
seq0007        ------------AAAGGATGCTCGTGGCATTTTATTCCAAGGTCAGT-ACATCT--TATA
seq0008        ------------AAAGGACG-CCGTGGCATTATATTCCAAAGTCATA-ACATCT--TAAT
seq0009        ------------AAAGGACG-CCGTGGCATTGTATCCCAAAGTCATT-ACATCT--TATA
seq0013        -CTCGGACGCCGAAACATTG-TCG---------ATTCCAAAATCATT-ATATCTGCTTGT
seq0014        ------------AAATGTGC-TCA---------CATGACCAAGCA-G-ACATTTGATGGA
seq0015        ------------CAAGGACG-TGC---------ACTGAAC-------------TGCTAGG
seq0018        C-----------AAAGGTCG-TCGTAACATTGGGTTGAAATGCCATT-GTGTCC--TCAC
seq0020        C-----------AAAGGAGG-TCGTAACGTTGTACTCAAATGTCATTCACCTCT--TCAA

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        AGGTTCG---------TCC---TGTCAG-------TTAGCATCCATGCC-CTATGACCTG
seq0001        AGGTTCG---------TCC---TGTCAG-------TTAGCATCCATGCC-CTATGACATG
seq0002        AGGTGCG---------TCC---TGTCAG-------TTAGCATCCGTGCC-CTAGGACCTG
seq0003        AGGTTCG---------TCC---TGTCAG-------TTAGCATCCGTGCC-CTATGACCTG
seq0004        AGGTTCG---------TCC---TGTCAG-------TTAGCATCCGTGCC-CTATGACCTG
seq0005        AGGTATG---------TCC---TGTCAG-------TTAGCATCCATGCC-GTATGACCTG
seq0006        AGGTTCG---------TCC---TGTCAG-------TTAGAATCCATGCC-GTATGACATG
seq0007        AGGTTCA---------TCC---TGTCAG-------TTAGCTTCCATGCC-GTATGACCTG
seq0008        AAGTTCG----------------------------------TTCCT------ATGACCTC
seq0009        ATGCTCG---------CCC---TGTCAG-------TTAACTTACCTGAC---TGGACCTC
seq0013        TGCTCCGGTCGGATGCCATGAATCCCCACACCTACTTA--AACTGGCACA--ACGTCTTC
seq0014        CG-TC--GTACCATTCTGCTAATGCCAATAAATCATCA--TTTTGTCGTA--CTGTCATT
seq0015        AATTCACGTAACATTGTAT---TCTAAGGTCATACTTAGCTTCCATGACT--ATGACCTC
seq0018        ATGTTCG---------TTC---TGTCGT-------TTAGCTTCCATGACG--AGAACCTT
seq0020        ATGTTGG---------TCG---TGGCAG-------TTTGCTTGAATGACT--AAGGCGTC

(position)     111111111111111111111111111111111111111111111111111111111111
               222222222233333333334444444444555555555566666666667777777777
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        CATTAGAATCCAGAATGGCGAACCTCGACATTCCAGAG-GTT----C--TCGTTTGACGG
seq0001        CATTAGAATCCAGAATGGCGAACCTCGACATTCGAGAG-TTT----C--TCGTTTGACGG
seq0002        CATTAGAATCCAGAATGGCGATCCTCGATATTCGAGAG-GTT----C--TCGTTTTACGG
seq0003        CATTAGAATGCCGAATGGCGATCCTCGATATTCGAGAG-GTT----C--TCGTTTGACGG
seq0004        CATTAGAATCCAGAATGGCGATCCTCGATATTCGAGAG-GTT----C--TCGTTTGACGG
seq0005        CATTAGAATCCAGAATGGCGGGCATCCATATACGAGAG-TTT----C--TCGTTCGACGT
seq0006        CAGTAGAATCCAGAATGGCGGGCCTCCATATTCGGGAG-TTT----C--TCGTTTGACGC
seq0007        CATTAGAATCCAGAATGGCGGGTCTCCATATTCGGGAG-TTT----C--TCGTTTGACGT
seq0008        CATTAGTA-CCAGAACGGCGACAGTCCACATTGGAGAG-CAT----CC-TTGTTTGACGG
seq0009        CATTAGAG-CCAGAATGGCGACA-CCCATAGTGGGCAG-CTT----CC-TTGATTGACTG
seq0013        CAGTAGGA-GCAGACGCGCAAGGGCCCATATTACCGTGTCATTCCGCCATTGTTTGACGG
seq0014        ---TAGGT-TCCAAGA--CTATGCCCTCCATT-------CGTAGCGAC-TTGCGAGAC-T
seq0015        CATTAGAA-GCAGACTGGCGAGACTCCATATTTCAGAGGATT----CC-TTGTATCACGG
seq0018        GATTCGCA--CAGACTGTCTACACTCCATATT-CAGAGTCTT----TC-GTGCTTGACTG
seq0020        T-TTTGAA-GCAGACTGGCAATACTCCTTATT-GAGAGTCGC----TC-TTGCCAGTCGG

(position)     11111111111111111111222
               88888888889999999999000
               01234567890123456789012
                                      
seq0000        CCACTGCC---ATGTGCACAGAG
seq0001        CCACTGAC---ATGTGCACAGAG
seq0002        CCACTGAC---ATGTGCACAGAG
seq0003        CCACTGAC---ATGTGCACAGAG
seq0004        CCTCTGAC---ATGTGCACAGAG
seq0005        CCACTGAC---ATGTGCCCAGAG
seq0006        CCACTGACGTCATGTGCCCAGAG
seq0007        CCACTGACGTCATGTGCCCAGAG
seq0008        CCACGGC-------TGCACAGAG
seq0009        CCCCGGC-------TGCACAGAG
seq0013        CCACTGC-------TCCACCGAG
seq0014        CCATATT-------TC-------
seq0015        CCACTGC-------T--AAAGAG
seq0018        CCAATGC-------TGCACAAAA
seq0020        A-ACTGC-------TGCACAGAG


<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<< Output of 'map_shifts_respos_bw_2msas' >>

($shift_lf, $shift_rf) = (0, -47) .

[ Shifts in the Reconstructed MSA ]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -   11   11   11   11  -19  -19  -19  -19    -  -19  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43    -  -42  -43
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -   11   11   11   11  -19  -19  -19  -19    -  -19  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43    -  -42  -43
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -   11   11   11   11  -19  -19  -19  -19    -  -19  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43    -  -42  -43
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -   11   11   11   11  -19  -19  -19  -19    -  -19  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43    -  -42  -43
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -   11   11   11   11  -19  -19  -19  -19    -  -19  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43    -  -42  -43
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -   11   11   11   11  -19  -19  -19  -19  -19  -19  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43    -  -42  -43
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -   11   11   11   11  -19  -19  -19  -19  -19  -19  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43    -  -42  -43
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -   11   11   11   11  -19  -19  -19  -19  -19  -19  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43    -  -42  -43
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -   11   11   11   11  -19  -19  -19  -19    -  -19  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43    -  -42  -43
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -   11   11   11   11  -19  -19  -19  -19    -  -19  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43    -  -42  -43
seq0013   	    -    0    0    0    0  -30  -30  -30  -30  -31  -53  -53  -53  -53  -53  -53  -53  -53  -53  -53    -  -52  -52  -52    -    -    -    -    -    -    -    -    -  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43    -  -42  -43
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -   11   11   11   11   11   11   11   11    -   12   12   12    -    -    -    -    -    -    -    -    -   21   21   21   21   21   21   21   21   21   21   21   21    -   22    -   23   23
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -   11   11   11   11  -19  -19  -19  -19    -  -19  -19  -19    -    -    -    -    -    -    -    -    -  -10  -10  -10  -10  -10  -10  -10    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    -    -    -    -    -    -    -    -    -    -    -   11   11   11   11  -19  -19  -19  -19    -  -19  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43    -  -42  -43
seq0020   	    0    -    -    -    -    -    -    -    -    -    -    -   11   11   11   11  -19  -19  -19  -19    -  -19  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43  -43



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   97   98   99

seq0000   	  -43  -43  -43  -43    -    -  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41    -    -    -    -    -    -    -    -    -  -32  -32  -32    -    -    -  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -  -22  -22  -22  -22  -22
seq0001   	  -43  -43  -43  -43    -    -  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41    -    -    -    -    -    -    -    -    -  -32  -32  -32    -    -    -  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -  -22  -22  -22  -22  -22
seq0002   	  -43  -43  -43  -43    -    -  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41    -    -    -    -    -    -    -    -    -  -32  -32  -32    -    -    -  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -  -22  -22  -22  -22  -22
seq0003   	  -43  -43  -43  -43    -    -  -41  -41    -  -41  -41  -41  -41  -41  -41  -41  -41    -    -    -    -    -    -    -    -    -  -32  -32  -32    -    -    -  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -  -22  -22  -22  -22  -22
seq0004   	  -43  -43  -43  -43    -    -  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41    -    -    -    -    -    -    -    -    -  -32  -32  -32    -    -    -  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -  -22  -22  -22  -22  -22
seq0005   	  -43  -43  -43  -43    -    -  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41    -    -    -    -    -    -    -    -    -  -32  -32  -32    -    -    -  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -  -22  -22  -22  -22  -22
seq0006   	  -43  -43  -43  -43    -    -  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41    -    -    -    -    -    -    -    -    -  -32  -32  -32    -    -    -  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -  -22  -22  -22  -22  -22
seq0007   	  -43  -43  -43  -43    -    -  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41    -    -    -    -    -    -    -    -    -  -32  -32  -32    -    -    -  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -  -22  -22  -22  -22  -22
seq0008   	  -43  -43  -43  -43    -    -  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	  -43  -43  -43  -43    -    -  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41    -    -    -    -    -    -    -    -    -  -32  -32  -32    -    -    -  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -  -22  -22  -22  -22  -22
seq0013   	  -43  -43  -43  -43  -43  -43  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -45  -48  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49  -49    -    -
seq0014   	   23   23   23   23   23   23   23   23   23   23   23   23    -   23    1    -    -    3    3    3    3    3    3    3    3   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2   -2   -2   -2   -2   -2    -    -
seq0015   	    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    1    1    -    -    -    4    4    4    4    4    4    4    4    4    4    4    3    2  -22  -22  -22  -22  -22
seq0018   	  -43  -43  -43  -43    -    -  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41    -    -    -    -    -    -    -    -    -  -32  -32  -32    -    -    -  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -  -22  -22  -22  -22  -22
seq0020   	  -43  -43  -43  -43    -    -  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41    -    -    -    -    -    -    -    -    -  -32  -32  -32    -    -    -  -29  -29  -29  -29  -29  -29    -    -    -    -    -    -    -  -22  -22  -22  -22  -22



(position)	  100  101  102  103  104  105  106  107  108  109  110  111  112  113  114  115  116  117  118  119  120  121  122  123  124  125  126  127  128  129  130  131  132  133  134  135  136  137  138  139  140  141  142  143  144  145  146  147  148  149

seq0000   	  -22  -22  -22  -22  -22  -22  -22  -47  -47    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46
seq0001   	  -22  -22  -22  -22  -22  -22  -22  -47  -47    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46
seq0002   	  -22  -22  -22  -22  -22  -22  -22  -47  -47    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46
seq0003   	  -22  -22  -22  -22  -22  -22  -22  -47  -47    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46
seq0004   	  -22  -22  -22  -22  -22  -22  -22  -47  -47    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46
seq0005   	  -22  -22  -22  -22  -22  -22  -22  -47  -47    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46
seq0006   	  -22  -22  -22  -22  -22  -22  -22  -47  -47    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46
seq0007   	  -22  -22  -22  -22  -22  -22  -22  -47  -47    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46
seq0008   	    -   -7   -7   -7  -52  -52    -    -    -    -    -    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46
seq0009   	  -22  -22  -22  -22  -22  -22  -22  -48  -48    -    -    -  -45  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46    -  -45  -46  -46  -46  -46  -46
seq0013   	  -47  -47  -47  -47  -47  -47  -47  -48  -48  -48    -    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46
seq0014   	    0    0    0    0    0    0    0    0    0    0    -    -    2    2    2    2    2    2    2    2    -    -    -    5    5    5    5    5    -    6    6    6    6    6    6  -20    -    -  -18  -18  -18  -18  -18  -18  -18  -18  -18  -18  -18  -18
seq0015   	  -22  -22  -22  -22  -22  -22  -22  -48  -48  -48    -    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46
seq0018   	  -22  -22  -22  -22  -22  -22  -22  -48  -48  -48    -    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46    -    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46
seq0020   	  -22  -22  -22  -22  -22  -22  -22  -48  -48  -48    -    -  -46  -46  -46  -46  -46  -46  -46  -46  -46    -  -46  -46  -46  -46  -46  -46    -  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46



(position)	  150  151  152  153  154  155  156  157  158  159  160  161  162  163  164  165  166  167  168  169  170  171  172  173  174  175  176  177  178  179  180  181  182  183  184  185  186  187  188  189  190  191  192  193  194  195  196  197  198  199

seq0000   	  -46  -46  -46  -46  -46  -46  -46  -46    -  -47  -47  -47    -    -    -    -  -43    -    -  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47    -    -    -  -47  -47  -47  -47  -47  -47  -47  -47  -47
seq0001   	  -46  -46  -46  -46  -46  -46  -46  -46    -  -47  -47  -47    -    -    -    -  -43    -    -  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47    -    -    -  -47  -47  -47  -47  -47  -47  -47  -47  -47
seq0002   	  -46  -46  -46  -46  -46  -46  -46  -46    -  -47  -47  -47    -    -    -    -  -43    -    -  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47    -    -    -  -47  -47  -47  -47  -47  -47  -47  -47  -47
seq0003   	  -46  -46  -46  -46  -46  -46  -46  -46    -  -47  -47  -47    -    -    -    -  -43    -    -  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47    -    -    -  -47  -47  -47  -47  -47  -47  -47  -47  -47
seq0004   	  -46  -46  -46  -46  -46  -46  -46  -46    -  -47  -47  -47    -    -    -    -  -43    -    -  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47    -    -    -  -47  -47  -47  -47  -47  -47  -47  -47  -47
seq0005   	  -46  -46  -46  -46  -46  -46  -46  -46    -  -47  -47  -47    -    -    -    -  -43    -    -  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47    -    -    -  -47  -47  -47  -47  -47  -47  -47  -47  -47
seq0006   	  -46  -46  -46  -46  -46  -46  -46  -46    -  -47  -47  -47    -    -    -    -  -43    -    -  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47
seq0007   	  -46  -46  -46  -46  -46  -46  -46  -46    -  -47  -47  -47    -    -    -    -  -43    -    -  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47
seq0008   	  -46  -46  -46  -46  -46  -46  -46  -46    -  -47  -47  -47    -    -    -    -  -43  -48    -  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -54    -    -    -    -    -    -    -  -47  -47  -47  -47  -47  -47
seq0009   	  -46  -46  -46  -46  -46  -46  -46  -46    -  -47  -47  -47    -    -    -    -  -43  -48    -  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -54    -    -    -    -    -    -    -  -47  -47  -47  -47  -47  -47
seq0013   	  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -54    -    -    -    -    -    -    -  -47  -47  -47  -47  -47  -47
seq0014   	  -18  -18    -    -    -    -    -    -    -  -11  -11  -11  -11  -12  -12  -13  -13  -13    -  -12  -12  -12  -12  -12  -12  -12  -12  -12    -  -11  -11  -11  -11  -11  -11  -11  -11    -    -    -    -    -    -    -   -4   -4    -    -    -    -
seq0015   	  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46  -46    -    -    -    -  -42  -42    -  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -54    -    -    -    -    -    -    -  -47    -    -  -47  -47  -47
seq0018   	  -46  -46    -  -46  -46  -46  -46  -46  -46  -46  -46  -46    -    -    -    -  -42  -42    -  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -54    -    -    -    -    -    -    -  -47  -47  -47  -47  -47  -47
seq0020   	  -46  -46    -  -46  -46  -46  -46  -46  -46  -46  -46  -46    -    -    -    -  -42  -42    -  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47  -47    -  -47  -47  -47  -47  -54    -    -    -    -    -    -    -  -47  -47  -47  -47  -47  -47



(position)	  200  201  202

seq0000   	  -47  -47  -47
seq0001   	  -47  -47  -47
seq0002   	  -47  -47  -47
seq0003   	  -47  -47  -47
seq0004   	  -47  -47  -47
seq0005   	  -47  -47  -47
seq0006   	  -47  -47  -47
seq0007   	  -47  -47  -47
seq0008   	  -47  -47  -47
seq0009   	  -47  -47  -47
seq0013   	  -47  -47  -47
seq0014   	    -    -    -
seq0015   	  -47  -47  -47
seq0018   	  -47  -47  -47
seq0020   	  -47  -47  -47




[INFORMATION] The original $commoner_shift_flank = -47. Thus, we will shift the entire reconstructed MSA ...

<< REVISED Output of 'map_shifts_respos_bw_2msas' >>

New ($shift_lf, $shift_rf) = (0, 0) .

[ New Shifts in the Reconstructed MSA ]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   47   47
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   47    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   47    -    -



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   97   98   99

seq0000   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0001   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0002   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0003   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0004   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0005   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28   28   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0006   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28   28   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0007   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28   28   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0008   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0009   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0013   	   47   47   17   17   17   17   16   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6    -   -5   -5   -5    -    -    -    -    -    -    -    -    -    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0014   	    -    -    -    -    -    -    -    -    -   58   58   58   58   58   58   58   58    -   59   59   59    -    -    -    -    -    -    -    -    -   68   68   68   68   68   68   68   68   68   68   68   68    -   69    -   70   70   70   70   70
seq0015   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28   28   28    -    -    -    -    -    -    -    -    -   37   37   37   37   37   37   37    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    -    5    4    4    4    4
seq0020   	    -    -    -    -    -    -    -    -    -   58   58   58   58   28   28   28   28    -   28    6    6    6    6    6    6    6    6    6    6    6    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4



(position)	  100  101  102  103  104  105  106  107  108  109  110  111  112  113  114  115  116  117  118  119  120  121  122  123  124  125  126  127  128  129  130  131  132  133  134  135  136  137  138  139  140  141  142  143  144  145  146  147  148  149

seq0000   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0001   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0002   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0003   	    4    -    -    6    6    -    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0004   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0005   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0006   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0007   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0008   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   40   40
seq0009   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0013   	    4    4    4    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2    2   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -    0    0    0
seq0014   	   70   70   70   70   70   70   70   70   70    -   70   48    -    -   50   50   50   50   50   50   50   50   46   46   46   46   46   46   46   46   46   46   46   46   46   46   46   45   45   45   45   45   45   45   45    -    -   47   47   47
seq0015   	   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   48   48    -    -    -   51   51   51   51   51   51   51   51   51   51   51   50   49   25   25   25   25   25   25   25   25
seq0018   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25
seq0020   	    4    -    -    6    6    6    6    6    6    6    6    6    6    6    -    -    -    -    -    -    -    -    -   15   15   15    -    -    -   18   18   18   18   18   18    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25



(position)	  150  151  152  153  154  155  156  157  158  159  160  161  162  163  164  165  166  167  168  169  170  171  172  173  174  175  176  177  178  179  180  181  182  183  184  185  186  187  188  189  190  191  192  193  194  195  196  197  198  199

seq0000   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0001   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0002   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0003   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0004   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0005   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0006   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0007   	   25   25   25   25    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0008   	   40   -5   -5    -    -    -    -    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0009   	   25   25   25   25   -1   -1    -    -    -    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    2    1    1    1    1    1    1    1    1
seq0013   	    0    0    0    0   -1   -1   -1    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0014   	   47   47   47   47   47   47   47    -    -   49   49   49   49   49   49   49   49    -    -    -   52   52   52   52   52    -   53   53   53   53   53   53   27    -    -   29   29   29   29   29   29   29   29   29   29   29   29   29   29    -
seq0015   	   25   25   25   25   -1   -1   -1    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0018   	   25   25   25   25   -1   -1   -1    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -
seq0020   	   25   25   25   25   -1   -1   -1    -    -    1    1    1    1    1    1    1    1    1    -    1    1    1    1    1    1    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -



(position)	  200  201  202  203  204  205  206  207  208  209  210  211  212  213  214  215  216  217  218  219  220  221  222  223  224  225  226  227  228  229  230  231  232  233  234  235  236  237  238  239  240  241  242  243  244  245  246  247  248  249

seq0000   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0
seq0002   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0
seq0006   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0007   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0008   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -7    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0009   	    1    1    1    1    1    -    0    0    0    -    -    -    -    4   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -7    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0013   	    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -7    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0014   	    -    -    -    -    -    -   36   36   36   36   35   35   34   34   34    -   35   35   35   35   35   35   35   35   35    -   36   36   36   36   36   36   36   36    -    -    -    -    -    -    -   43   43    -    -    -    -    -    -    -
seq0015   	    1    1    1    1    1    1    1    1    1    -    -    -    -    5    5    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -7    -    -    -    -    -    -    -    0    -    -    0    0    0    0    0    0
seq0018   	    1    1    1    1    1    1    1    1    1    -    -    -    -    5    5    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -7    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0
seq0020   	    1    1    1    1    1    1    1    1    1    -    -    -    -    5    5    -    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0   -7    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0



<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<< Output of 'br_list_classes_shift_respos' >>

$commoner_shift_flank = 0 .


<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

... NO CHANGES were made ...


<<<<< Preliminary (4): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<< Output of 'lump_together_similar_blocks': Content of @{$composite_miniblocks} (#{composite_miniblocks} = 45) >>

Indx_cmp_miniblock	beg_cmb	end_cmb	mrca	indices,constituent,miniblocks	list,position,shifts	merger,types	indices,involved,seqs

0	47	47	29	50	47	n/a	13,14
1	48	70	20	52,33,32,1,2	47,17,16,-6,-5	0,0,0,0	10
2	59	62	29	63	58	n/a	0,1,2,3,4,5,6,7,8,9,12,13,14
3	59	91	21	64,65,66	58,59,68	0,0	11
4	63	79	29	37,29	28,6	0	0,1,2,3,4,5,6,7,8,9,13,14
5	63	86	23	38,45	28,37	0	12
6	80	93	27	22	4	n/a	0,1,2,3,4,5,6,7,8,9,10,13
7	80	100	28	24	4	n/a	14
8	93	111	21	67,68,54	69,70,48	0,0	11
9	95	95	27	28	5	n/a	0,1,2,3,4,5,6,7,8,9,10,13
10	96	100	27	23	4	n/a	0,1,2,3,4,5,6,7,8,9,13
11	96	102	20	26	4	n/a	10
12	100	139	23	57,53,60	50,48,51	0,0	12
13	103	113	29	30	6	n/a	0,1,2,3,4,5,6,7,8,9,13,14
14	103	118	20	21	2	n/a	10
15	114	121	21	59	50	n/a	11
16	119	119	20	8	-1	n/a	10
17	120	153	20	4,12	-2,0	0	10
18	122	166	21	49,48,51,56	46,45,47,49	0,0,0	11
19	123	134	29	31,34	15,18	0	0,1,2,3,4,5,6,7,9,13,14
20	140	141	23	58,55	50,49	0	12
21	142	153	29	35	25	n/a	0,1,2,3,4,5,6,7,9,12,13,14
22	148	150	16	46	40	n/a	8
23	151	152	16	3	-5	n/a	8
24	154	204	15	11,14	0,1	0	0,1,2,3,4,5,6,7
25	154	156	29	5	-1	n/a	10,12,13,14
26	154	155	17	7	-1	n/a	9
27	159	215	20	17	1	n/a	10
28	159	208	29	13	1	n/a	12,13,14
29	159	204	16	18	1	n/a	8
30	159	159	17	19	2	n/a	9
31	160	189	17	15	1	n/a	9
32	170	181	21	61,62	52,53	0	11
33	182	182	21	36	27	n/a	11
34	185	198	21	39	29	n/a	11
35	191	191	17	20	2	n/a	9
36	192	204	17	16	1	n/a	9
37	206	213	19	10,25	0,4	0	0,1,2,3,4,5,6,7,8,9
38	206	211	21	43,41	36,35	0	11
39	212	224	21	40,42	34,35	0	11
40	213	214	29	27	5	n/a	12,13,14
41	214	214	18	6	-1	n/a	8,9
42	226	233	21	44	36	n/a	11
43	233	233	29	0	-7	n/a	8,9,10,12,13,14
44	241	242	21	47	43	n/a	11



<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<< (1) For Reference MSA >>>

<<< (2) For Reconstructed MSA >>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 45) >>>>>


[[ Results of the Main Process (1st Round) ]]

[ Contents of @cblk_wise_cts_invlvd_indels ]

Indx_cmp_blk	#{rlv_indels}_ref	#{rlv_indels}_rec	#{rltd_indels}_ref	#{rltd_indels}_rec	#{other_involved}_ref	#{other_involved}_rec

0	0	0	0	0	0	0
1	1	1	0	0	0	0
2	0	0	1	1	0	0
3	1	1	0	1	0	0
4	0	1	0	0	0	0
5	1	1	0	0	0	0
6
7	1	1	0	0	0	0
8	1	3	0	0	0	0
9
10	0	1	0	0	0	0
11	1	0	0	0	0	0
12	2	1	0	0	0	0
13	0	2	0	0	0	0
14	2	0	0	0	0	0
15	1	1	0	0	0	0
16	2	0	0	0	0	0
17	2	0	0	0	0	0
18	0	1	1	0	0	0
19
20	2	0	0	1	0	0
21	0	1	3	1	0	0
22	1	1	0	0	0	0
23	1	1	1	0	0	0
24	1	1	1	1	0	0
25	0	1	1	1	0	0
26	0	0	0	1	0	0
27	1	1	0	0	0	0
28	0	1	0	0	0	0
29	0	1	1	0	0	0
30	1	0	0	1	0	0
31	1	1	0	0	0	0
32	0	1	1	0	0	0
33	0	1	1	0	0	0
34	0	2	0	0	0	0
35	1	1	0	0	0	0
36	1	0	0	0	0	0
37	1	1	1	1	0	0
38	1	1	0	0	0	0
39	1	1	0	0	0	0
40	0	1	1	1	0	0
41	1	0	0	1	0	0
42	0	1	0	0	0	0
43	1	1	0	0	0	0
44	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 4): 0, 6, 9, 19 . ]


[ Contents of @cblk_wise_msa_errors ]

Indx_cmp_blk	Indx_error	len_cblk_ref	len_cblk_rec	Type	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(ref)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(rec)

0	Skipped!!(NO_ASSOCIATED_EVENT(???))
1	0	75	23	Complex(???)	20:74:75:-	20:48:58:-
2	0	4	4	Complex(???)	21:5:34:-	20:48:58:-
3	0	23	33	Complex(???)	21:5:34:-	21:92:92:X/20:48:58:-
4	0	39	17	Complex(???)	None	24:71:79:X
5	0	15	24	Complex(???)	23:41:62:-	23:87:99:X
6	Skipped!!(NO_RELEVANT_BRANCH)
7	0	21	21	Shift(???)	28:91:91:-	28:94:94:-
8	0	40	19	Complex	21:5:34:-	21:92:92:X/21:112:113:X/21:109:109:X
9	Skipped!!(NO_RELEVANT_BRANCH)
10	0	5	5	Complex(???)	None	24:101:102:-
11	0	7	7	Complex(???)	20:99:100:X	None
12	0	39	40	Complex(???)	23:89:89:X/23:41:62:-	23:87:99:X
13	0	11	11	Complex(???)	None	24:101:102:-/24:114:122:-
14	0	16	16	Complex(???)	20:99:100:X/20:117:119:X	None
15	0	8	8	Shift	21:72:73:X	21:112:113:X
16	0	1	1	Complex(???)	20:117:119:X/20:121:121:X	None
17	0	32	34	Complex(???)	20:121:121:X/20:129:153:-	None
18	0	42	45	Complex(???)	20:74:75:-	21:167:169:X
19	Skipped!!(NO_RELEVANT_BRANCH)
20	0	3	2	Complex	23:89:89:X/23:93:116:X	24:135:141:-
21	0	12	12	Complex	23:93:116:X/20:129:153:-/20:117:119:X	22:145:146:X/24:135:141:-
22	0	3	3	Complex(???)	16:111:155:X	16:123:147:X
23	0	2	2	Complex(???)	16:111:155:X/17:158:158:X	16:153:155:X
24	0	50	51	Partial-Split(gap-aligned)(?)	15:154:154:-/19:204:205:X	15:157:158:-/19:205:205:X
25	0	3	3	Complex(???)	15:154:154:-	19:156:156:X/15:157:158:-
26	0	2	2	NO_ASSOCIATED_EVENT(???)	None	16:153:155:X
27	0	57	57	Complex(???)	20:210:214:-	20:215:215:-
28	0	50	50	Complex(???)	None	22:209:212:-
29	0	46	46	Complex(???)	17:158:158:X	16:153:155:X
30	0	1	1	Complex(???)	17:158:158:X	16:153:155:X
31	0	30	30	Shift	17:158:158:X	17:190:190:X
32	0	11	12	Complex(???)	20:129:153:-	21:167:169:X
33	0	1	1	Complex(???)	20:129:153:-	21:183:184:X
34	0	14	14	Complex(???)	None	21:183:184:X/21:199:205:X
35	0	1	1	Shift	17:190:190:X	17:190:190:X
36	0	13	13	Complex(???)	17:190:190:X	None
37	0	4	8	Complex(???)	19:204:205:X/18:215:215:-	19:205:205:X/15:214:214:X
38	0	7	6	Complex(???)	21:177:177:X	21:199:205:X
39	0	12	13	Shift	21:177:177:X	21:225:225:X
40	0	2	2	Complex(???)	20:210:214:-	22:209:212:-/20:215:215:-
41	0	1	1	Complex(???)	18:215:215:-	15:214:214:X
42	0	8	8	Complex(???)	None	21:225:225:X
43	0	1	1	Shift	15:233:239:-	15:234:240:-
44	0	2	2	Complex(???)	21:200:249:X	21:243:249:X


[ Contents of %indel_ref2assoc_cblks ]

Br:beg:end(ref)	indices,of,associated,composite-blocks

25:0:0	{Equivalent to '25:47:47'(rec)}
21:5:34	2,3,8
14:39:39	{Equivalent to '14:67:67'(rec)}
23:41:62	5,12
21:72:73	15
20:74:75	1,18
23:89:89	12,20
28:91:91	7
23:93:116	20,21
20:99:100	11,14
5:99:99	{Equivalent to '5:105:105'(rec)}
16:111:155	22,23
20:117:119	14,16,21
20:121:121	16,17
20:129:153	17,21,32,33
15:154:154	24,25
17:158:158	23,29,30,31
27:167:167	None
15:174:174	{Equivalent to '15:175:175'(rec)}
26:175:175	None
21:177:177	38,39
17:190:190	35,36
25:198:198	None
21:200:249	44
19:204:205	24,37
20:210:214	27,40
18:215:215	37,41
27:228:228	None
15:233:239	43
13:235:237	{Equivalent to '13:235:237'(rec)}
23:242:243	None


[ Contents of %indel_rec2assoc_cblks ]

Br:beg:end(rec)	indices,of,associated,composite-blocks

25:47:47	{Equivalent to '25:0:0'(ref)}
20:48:58	1,2,3
14:67:67	{Equivalent to '14:39:39'(ref)}
24:71:79	4
23:87:99	5,12
21:92:92	3,8
28:94:94	7
24:101:102	10,13
5:105:105	{Equivalent to '5:99:99'(ref)}
21:109:109	8
21:112:113	8,15
24:114:122	13
16:123:147	22
22:126:128	None
24:135:141	20,21
22:145:146	21
16:153:155	23,26,29,30
19:156:156	25
15:157:158	24,25
21:167:169	18,32
27:168:168	None
15:175:175	{Equivalent to '15:174:174'(ref)}
26:176:176	None
21:183:184	33,34
17:190:190	31,35
25:199:199	None
21:199:205	34,38
19:205:205	24,37
22:209:212	28,40
15:214:214	37,41
20:215:215	27,40
21:225:225	39,42
27:228:228	None
15:234:240	43
13:235:237	{Equivalent to '13:235:237'(ref)}
23:242:243	None
21:243:249	44


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>

[[ Interim Results ]]

[ Contents of %cb2hard_linked (#{keys} = 2) ]

Indx_cmp_blk	=> [indices,cblks,hard,linked,by,the,key]

2	=> [3],
6	=> [7],


[ Contents of %cb2hard_linking (#{keys} = 2) ]

Indx_cmp_blk	=> [indices,cblks,hard,linking,the,key]

3	=> [2],
7	=> [6],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 4) ]

Indx_cblk_A	indx_cblk_B

10	13
24	25
35	36
39	42


[[ Results of the Main Process (2nd Round) ]]

[ For the 1 th pair: (10, 13) ]

[ For the 2 th pair: (24, 25) ]


{ The representative path is: 24  -> 25 }


( Rough frameworks of the 1st- & 2nd-moved c-blocks )

Subject_c-block	beg_cb	end_cb	shift_le	shift_re	rlv_branch	indices,invlvd,seqs,le	indices,invlvd,seqs,re

1st(intermediate)	157	204	1	1	15	0,1,2,3,4,5,6,7	0,1,2,3,4,5,6,7
2nd(reconstructed)	154	156	-1	-1	19	10,12,13,14	10,12,13,14


( Errors associated with the c-blocks )

Subject_c-block	Type	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex	19:204:205:X	15:158:158:-/19:156:156:X/19:205:205:X/18:157:157:X
2nd(reconstructed)	Complex	19:156:156:X/25:154:154:-/15:158:158:-/18:157:157:X	19:156:156:X/15:157:158:-


[ For the 3 th pair: (35, 36) ]

[ For the 4 th pair: (39, 42) ]

